diff --git a/_countit/batch_bed2wig.pl b/_countit/batch_bed2wig.pl
index 32ee9af..ec48a9e 100755
--- a/_countit/batch_bed2wig.pl
+++ b/_countit/batch_bed2wig.pl
@@ -8,6 +8,8 @@
 
 use Carp;
 use Data::Dumper;
+
+use MyConfig;
 use Quantas;
 
 my $prog = basename ($0);
@@ -18,7 +20,13 @@
 my $suffix = "";
 my $inputFormat = "bed";
 my $weight = "";
-my $cache = "";
+my $qsub = 0;
+my $queueName = "";
+my $jobName = "job";
+
+my $cache = getDefaultCache ($prog);
+my $keepCache = 0;
+
 
 #my $method = "mean";  #sum
 
@@ -27,6 +35,9 @@
 	"weight"=>\$weight,
 	"base:s"=>\$base,
 	"suffix:s"=>\$suffix,
+	"qsub"=>\$qsub,
+	"queue:s"=>\$queueName,
+	"job:s"=>\$jobName,
 	"cache:s"=>\$cache,
 	"v|verbose"=>\$verbose
 );
@@ -35,12 +46,16 @@
 {
 	print "generate expression matrix\n";
 	print "Usage $prog [options] <in.conf> <outdir>\n";
-	print " -format       [string] : input format ([bed]|bedgraph), gz or bz2 files are accepted\n";
-	print " -weight       [string] : weight individual tags (for bed files only; bedgraphs are always weighted)\n";
-	print " -base         [string] : base dir of input data\n";
-	print " -suffix       [string] : add suffix to the file names\n";
-	print " -cache        [string] : cache dir\n";
-	print " -v                     : verbose\n";
+	print " --format       [string] : input format ([bed]|bedgraph), gz or bz2 files are accepted\n";
+	print " --weight       [string] : weight individual tags (for bed files only; bedgraphs are always weighted)\n";
+	print " --base         [string] : base dir of input data\n";
+	print " --suffix       [string] : add suffix to the file names\n";
+	print " --qsub                  : run jobs using sge\n";
+	print " --queue        [string] : queque name\n";
+	print " --job          [string] : job name\n";
+	print " --cache        [string] : cache dir\n";
+	print " --keep-cache            : keep cache dir\n";
+	print " -v                      : verbose\n";
 	exit (1);
 }
 
@@ -51,7 +66,6 @@
 Carp::croak "incorrect input format: $inputFormat\n" if $inputFormat ne 'bed' && $inputFormat ne 'bedgraph';
 
 
-
 print "loading configuration file from $configFile ...\n" if $verbose;
 Carp::croak "contig file $configFile does not exist\n" unless -f $configFile;
 my $groups = readExprConfigFile ($configFile, $base, $suffix);
@@ -64,7 +78,19 @@
 print "generating wig files for each group...\n" if $verbose;
 my @groupNames = sort {$groups->{$a}->{"id"} <=> $groups->{$b}->{"id"}} keys %$groups;
 
+system ("mkdir $cache");
+
 my $iter = 0;
+my $scriptListFile = "$cache/script.list";
+my $scriptDir = "$cache/scripts";
+
+my $fout;
+if ($qsub)
+{
+	open ($fout, ">$scriptListFile") || Carp::croak "cannot open $scriptListFile to write\n";
+	system ("mkdir $scriptDir");	
+}
+
 foreach my $gName (@groupNames)
 {
 	my $samples = $groups->{$gName}->{"samples"};
@@ -80,29 +106,64 @@
 		$cmd = "bzcat ";
 	}
 
-	foreach my $s (@$samples)
+	my $outputFile = "$outDir/$gName";
+	$outputFile .= $suffix if $suffix ne "";
+	
+	if (@$samples == 1 && $inputFormat eq 'bedgraph')
 	{
-		print "$iter: group=$gName, sample=$s\n" if $verbose;
-		my $inputFile = $s;
+		#only one bedgraph file, we just make a copy
+		my $inputFile = $samples->[0];
 		$inputFile = "$base/$inputFile" if $base ne '';
+
+		$cmd = "cp $inputFile $outputFile";
+	}
+	else
+	{
+		foreach my $s (@$samples)
+		{
+			print "$iter: group=$gName, sample=$s\n" if $verbose;
+			my $inputFile = $s;
+			$inputFile = "$base/$inputFile" if $base ne '';
 		
-		$cmd .= " $inputFile";
+			$cmd .= " $inputFile";
+		}
+
+		if ($inputFormat eq 'bedgraph')
+		{
+			$cmd .= " | awk '{print \$1\"\\t\"\$2\"\\t\"\$3\"\\tt\\t\"\$4}'";
+		}
+
+		my $weightFlag = $inputFormat eq 'bedgraph' || $weight ? '--weight' : '';
+		$cmd .= " | perl $cmdDir/tag2profile.pl $verboseFlag -c $cache/tag2profile_$iter $weightFlag -big -exact -of bedgraph - $outputFile";
 	}
 
-	if ($inputFormat eq 'bedgraph')
+	print $cmd, "\n";
+	
+	if ($qsub)
 	{
-		$cmd .= " | awk '{print \$1\"\\t\"\$2\"\\t\"\$3\"\\tt\\t\"\$4}'";
+		my $scriptFile = "$scriptDir/script_$iter.sh";
+		my $fout2;
+		open ($fout2, ">$scriptFile") || Carp::croak "cannot open file $scriptFile to write\n";
+		print $fout2 $cmd, "\n";
+		close ($fout2);
+		print $fout $scriptFile, "\n";
 	}
+	else
+	{
+		my $ret = system ($cmd);
+		Carp::croak "CMD=$cmd failed:$?\n" if $ret != 0;
+	}
+	$iter++;
+}
 
-	my $weightFlag = $inputFormat eq 'bedgraph' || $weight ? '--weight' : '';
-	my $cacheFlag = $cache ne ''? "-c $cache" : '';
-	$cmd .= " | perl $cmdDir/tag2profile.pl $verboseFlag $cacheFlag $weightFlag -big -exact -of bedgraph - $outDir/$gName.wig";
-
-	print $cmd, "\n";
-	my $ret = system ($cmd);
-	Carp::croak "CMD=$cmd failed:$?\n" if $ret != 0;
+if ($qsub)
+{
+	close ($fout);
 
-	$iter++;
+	my $cmd = "perl $cmdDir/batchQsub.pl $verboseFlag -c $cache/qsub -j $jobName -q $queueName --wait $scriptListFile";
+	print $cmd, "\n" if $verbose;
+	system ($cmd);
 }
 
+system ("rm -rf $cache") unless $keepCache;
 
diff --git a/_countit/gen_expression_matrix.pl b/_countit/gen_expression_matrix.pl
index 3975246..161f5b3 100755
--- a/_countit/gen_expression_matrix.pl
+++ b/_countit/gen_expression_matrix.pl
@@ -50,18 +50,21 @@
 
 print "done.\n" if $verbose;
 
-print "loading data of individual samples ...\n" if $verbose;
+print "loading data of individual samples and aggregating samples in the same group...\n" if $verbose;
 
-my %sampleData;
+#my %sampleData;
 my $geneId;
 my $n = 0;
 my $iter = 0;
 my $geneInfo;
 
 my @groupNames = sort {$groups->{$a}->{"id"} <=> $groups->{$b}->{"id"}} keys %$groups;
+my @groupData;
 
-foreach my $gName (@groupNames)
+for (my $g = 0; $g < @groupNames; $g++)
 {
+	my $gName = $groupNames[$g];
+
 	my $samples = $groups->{$gName}->{"samples"};
 	foreach my $s (@$samples)
 	{
@@ -78,28 +81,7 @@
 		{
 			$n = @$geneInfo;
 		}
-		$sampleData{$s} = $sdata->{"data"};
-		$iter++;
-	}
-}
-
-print "$iter samples, $n genes loaded.\n" if $verbose;
-
-
-print "aggregating samples in the same group ...\n" if $verbose;
-
-
-my @groupData;
-
-for (my $g = 0; $g < @groupNames; $g++)
-{
-	my $gName = $groupNames[$g];
-	my $samples = $groups->{$gName}->{"samples"};
-
-	foreach my $s (@$samples)
-	{
-		print "sample=$s\n" if $verbose;
-		my $data = $sampleData{$s};
+		my $data = $sdata->{"data"};
 		for (my $i = 0; $i < $n; $i++)
 		{
 			my $d = $data->[$i];
@@ -107,9 +89,11 @@
 			$groupData[$g][$i][0] += $d->[0]; #tagNum
 			$groupData[$g][$i][1] += $d->[1]; #RPKM
 		}
+		$iter++;
 	}
 }
 
+print "$iter samples, $n genes loaded.\n" if $verbose;
 
 my $fout;